- September 2015:
Thomas Sander now offers the organic
part of the COD
database for download on his website.
Thomas Sander from Actelion
has relased the DataWarrior
program as open-source!
The "FPSM method" uses
a Rietveld like fitting procedure to test all possible crystal
structures from the Crystallography Open Database, rank them and
find the more probable in your diffraction pattern. In the end a
Rietveld phase quantification is done with the phases
identified. The new paper is sumitted to the J. Appl. Cryst.
November 2014: The
new QUALX version
has been developed that can use COD data for search-match material
release of their COD-derived search-match database. The
new COD database file is meant to be used with version 3.0e or
higher of the PANalytical HighScore or HighScore Plus software
packages. It can be downloaded in two parts of ~1.4 Gb each from
August 2014: COD is added to the
of recommended data repositories by the Nature Publishing Group
journal Scientific Data.
August 2014: COD and TCOD were presented in a poster session of the
23rd Congress and General Assembly of the IUCr in Montreal,
Canada. The posters are stored in the
January 2014: During the visit of Peter Murray-Rust in the
University of Vilnius, Institute of Biotechnology, the COD was
merged with the data from CrystalEye, and started using Jumbo
Converters to generate lists of chemically interesting moyeties and
fragments. These lists are stored in
data directory, and will soon be available as an SQL database
and via the Web interface.
Two RSS feeds for exploring the COD have been launched:
"What's New on COD" and
"New Structures in COD". Both feeds
should be automatically detectable at
COD Home page. For browsers
that do not support RSS, COD feeds can be accessed using
web-based feed viewers like
"What's New on COD" and
"New Structures in COD".
Structure preview using JSmol,
cards. Now preview of COD structures is available on the platforms that do
not support Java (i.e. iPhone/iPad) or do not support applets (i.e.
Android). Structure preview using Jmol is still available via link 'Display
in Jmol' below the JSmol view.
search-match database with powder patterns from COD.
new release of the COD-derived search-match database. The new COD
database file is meant to be used with version 3.0a or higher of the
PANalytical HighScore or HighScore Plus software packages.
Search engine plugin for Firefox and IE7 Web browsers for querying the COD
is now available. When installed, the plugin places COD among the
browser's search engines (in Firefox 14.0.1, they are accessible in the
drop down list in the top-right corner of the brower's window). The plugin
allows querying the COD via textual and COD ID searches.
The plugin is based on OpenSearch description format, which is
compatible with Firefox and IE7 (we haven't tested the latter yet).
Firefox comes with autodiscovery feature, so to obtain the plugin,
the option "Add COD" should appear in the browser's drop down menu
containing search engines.
February 2012: a new edition of the COD database for search-match and structure
retrieval with PANalyticals HighScore and HighScore Plus software is
September 2011: Corrected COD database for search-match and structure
retrieval with PANalyticals HighScore and HighScore Plus software is
July 2011: Powder patterns for
the Rigaku software
January 2011: Powder patterns computed from COD
for Rigaku software.
December 2007: Further developments of the COD (and PCOD) will take place
in Lithuania, supervised by Dr. Saulius Gražulis, Institute of Biotechnology,
Graiciuno 8, LT-02241 Vilnius, Lietuva (Lithuania), and a student, Justas
Butkus, from the Vilnius
Gediminas Technical University.
New Web address: http://cod.ibt.lt/
September 2007: at its recent meeting the IUCr Executive Committee decided
that the CIFs associated with structural papers published in IUCr journals
should be made freely available to the databases, including COD. Thus COD
has permission to download these files from the IUCr site on a routine
February 2007: Creation of the P2D2
; Predicted Powder Diffraction Database
61015 entries - search-match possible with the EVA Bruker software
February 2007: Massive PCOD update
58500 entries added, see details
61132 total in PCOD
December 2006: COD update: ~48000 entries (~10000 from AMCSD)
June 2006: COD update: ~43000 entries
May 2006: COD update: ~40000 entries
April 2006: COD update: ~37000 entries (~9000 from AMCSD)
March 2006: COD update: ~34000 entries
February 2006: PCOD update with >1000 predicted titanosilicates: ~2600
January 2006: COD update: ~31000 entries
December 2005: COD update: ~28000 entries
November 2005: COD update: ~24000 entries
October 2005: COD update: ~20000 entries
~30 Volunteers declared wanting to help
New COD Advisory Board Members
Call to volunteers
September 2005: COD update: ~18000 entries (~8000 from AMCSD)
August 2005: poster
presented at the IUCr XX, Florence
June 2005: more than 1000 signatures to the petition.
May 2005: Petition
for Open Data in Crystallography
Asked for permission to ACS to copy systematically their CIF files.
Still no permission to copy the CIF files availaible for free at the Acta
Cryst. journals Web pages.
May 2004, EMC2, El Jadida, Morocco, conference (in French) on databases
- were assisting: Bill Duax as IUCr President, Claude Lecomte as former
ECA President. Both agreed that the PDB should be considered as a model,
with open access on the Web (pictures).
January 2004: added ~200 new entries in the PCOD (B2O3,
AlF3, BxSiyOz, BxReyOz
predicted - or enumerated - by GRINSP
with R(DLS)< 0.01
January 2004: added ~400 new entries from AMCSD (5448 entries from AMCSD,
total entries: 12965)
December 2003: a subset of the COD is created: PCOD
(Predicted Crystallography Open Database). This is an attempt to gather
all these theoretical crystal structures which will very probably soon
exceed in number the really observed ones.
November 2003: added ~300 new CIFs from AMCSD
September 2003: the COD query for accessing or having a link towards the
IUCR CIFs failed (read the query and the
Conference on Open Access to the Data and Results of the Sciences and Humanities
20 - 22 Oct 2003, Berlin - http://www.zim.mpg.de/openaccess-berlin/index.html
August 2003: a tutorial is
written describing how to install the COD on your own computer (PC) and
running it in standalone conditions.
July 2003: The July 2003 2nd edition of the on-line IUCr Computing Commission
Newsletter on-line is available as an Acrobat PDF file (~2.6Meg and 57
pages) at: http://www.iucr.org/iucr-top/comm/ccom/newsletters/2003jul/
See inside a contribution about COD:
"How easy/hard is to convert raw data into a web database? - by
Armel Le Bail
July 2003: Crystal Impact, sponsor at the beginning (through Michael Berndt,
offering the www.crystallography.net
domain name) disengaged from the COD. The domain name is transferred under
the control of the COD.
Sad news about one of the main COD initiators, Michael Berndt.
By email from Dr. Klaus Brandenburg and Dr. Holger Putz:
Michael Berndt died on June 30th, 2003 after a long, serious illness
at the age of 39.
Michael studied chemistry and received his PhD in 1995 in the group
of Prof. Bergerhoff at the university of Bonn, Germany. Even during his
studies he was active in writing chemistry software. For the retrieval
software of the Inorganic Crystal Structure Database (ICSD), he won the
German-Austrian Academic Software Award in 1993. In 1997, he founded the
company Crystal Impact together with Dr. Klaus Brandenburg. Michael was
substantially involved in the development of the Browser software for the
Inorganic Materials Database "Pauling File". Based on his long-term experience
in this area, he started with a new, universally applicable system for
the simultaneous access to diverse crystallographic databases.
With Michael we lose an always competent, reliable and helpful colleague.
May 2003: 200 REF files added, mainly taken from the SDPD
database of references - Much more to come. The REF files can be
completed with atomic coordinates and transformed into CIFs by the REF2CIF
May 2003: CIFs do not have to be located at the COD server side.
If there is a CIF available somewhere in the Internet, the COD can provide
a link to it. Thus, we have created an option for datasets, called REF
files, that operate like a pointer. They contain minimal information, allowing
a search for cell parameters, volume, chemical formula, reference including
text in publication title, authors, journal, year. Therefore, one can now
deposit either CIF (preferably) or REF files to the COD. A REF file is
quite simple to make by a text editor. It contains 4 lines:
1- reference as complete as possible (or/and comments if any)
2- chemical formula with spaces (ex: C2 H6 O)
3- the 6 cell parameters in angstroms and dregrees: a b c alpha beta
gamma separated by one space
4- space group in Hermann Mauguin notation, no space
A REF file can contain a series of 4 lines (references + minimal crystal
data) separated by an empty line.
Example for 2 entries in the same REF file:
A.J. Mora, A.N. Fitch, The low-temperature crystal
structure of RS-camphor, J. Solid State Chem 134 (1997) 211-214
C10 H16 O
6.8341 11.6584 11.5000 90. 90. 90.
C. Feldmann, M. Jansen, To the knowledge of cis-sodium
hyponitrite, Z. Anorg. Allg. Chem. 623 (1997) 1803-1809
Na2 N2 O2
5.107 9.211 6.159 90. 97.91 90.
The REF files will be built very easily from your own list of publication
references with addition of the chemical formula, the cell parameters and
the space group.
April 2003: The IUCr is contacted for permission of downloading the IUCr
journals freely available CIFs.
Decision will be taken by the Executive
Committee in August 2003. As a test, the Acta Cryst. C 1991 and
1992 references + minimal crystal data pointing at the IUCr
existing CIFs are included in COD. The search result redirects
to the IUCr journals web site.
April 2003: Donation of > 1200 CIFs from IPMC. Thanks!
March 2003: A new Web page showing the logos
with links to the main Donators is set up.
March 2003: Donation of > 850 CIFs from the CRISMAT (Caen, France). Thanks
March 2003: First minimal search page
coded in PHP.
March 2003: Donation of 450 CIFs from the Laboratoire des Fluorures (Le
Mans, France). Thanks!
March 2003: Donation of 3725 CIFs from the American Mineralogist database
(Bob Downs). Thanks a lot!
March 2003: The CIF2COD program (FORTRAN)
is built up on the basis of CIF2SX from Louis Farrugia. Thanks! CIF2COD
read several CIFs (from n.cif to n+m.cif), performs several quality tests,
and produces a .txt file containing m+1 lines with the MySQL
database (cod) unique table (data) fields (entry, file, pdf, a,
b, c, alpha, beta, gamma, vol, nel, sg, formula, text).
March 6, 2003: The CryOD
Mailing List is open to the COD Advisory board members.
March 5, 2003: COD birth (announced at various mailing lists, Newsgroups,
and IUCr What's New Web page), starting after a discussion at the SDPD
Mailing List (February 12-14, 2003) and the writing of the crystallography
database quiz (removed now) - see various
Introductory text: Databases of crystal structure
atomic coordinates (most of them commercial databases) delay new data by
3, 6 months, if not much more (1, 2 years) after the publication. As a
crystallographer, you certainly are interested in having access as soon
as possible to new and old data, and why not for free. Your main reason
can be that you do not want to waste time in a structure redetermination
of an already known compound. The Internet offers possibilities for quasi
immediate answers, provided:
1. A small team of engaged scientists with some experience in database
and software design coordinate the Crystallography Open Database (COD)
project based on free and automated software a) for maintaining the database,
b) for data evaluation and calculation of derived data (e.g. calculated
powder pattern from crystal structures for search-match purposes), c) for
browsing and retrieval.
2. The authors (i.e. the scientific community = YOU) provide the project
with database entries (note, that if you have'nt sold your experimental
results exclusively, you are free to distribute the data to such a database,
even if they have already been part of a publication - and a lot of good
data have never been published).
We are not in the same situation as decades before when the well-known
databases (ICSD, CSD, PDF) started. Today we have the Internet, fast computers,
and a big pool of free available software. The question is : Do we have
enough scientists who are willing to cooperate ?
The COD, once finalized, will be nothing else than a keyword-searchable
Web server of crystal structure atomic coordinates, preserving the data
after publication as well as unpublished data.
Search the database